Uses of Class
org.biojava.nbio.core.alignment.template.AlignedSequence.Step

Packages that use AlignedSequence.Step

Package	Description
org.biojava.nbio.core.alignment
org.biojava.nbio.core.alignment.template

Uses of AlignedSequence.Step in org.biojava.nbio.core.alignment

Constructor parameters in org.biojava.nbio.core.alignment with type arguments of type AlignedSequence.Step

Constructor and Description
SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps) Creates a new AlignedSequence for the given AlignedSequence in a global alignment.
SimpleAlignedSequence(AlignedSequence<S,C> prev, List<AlignedSequence.Step> steps, int numBefore, int numAfter) Creates a new AlignedSequence for the given AlignedSequence in a local alignment.
SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps) Creates an AlignedSequence for the given Sequence in a global alignment.
SimpleAlignedSequence(S original, List<AlignedSequence.Step> steps, int numBefore, int numAfter) Creates an AlignedSequence for the given Sequence in a local alignment.
SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given profiles.
SimpleProfile(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given profiles.
SimpleProfile(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya) Creates a pair profile for the given sequences.
SimpleProfile(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya) Creates a pair profile for the given sequences.
SimpleProfilePair(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given profiles.
SimpleProfilePair(Profile<S,C> query, Profile<S,C> target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given profiles.
SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya) Creates a pair profile for the given sequences with a local alignment.
SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, int xb, int xa, List<AlignedSequence.Step> sy, int yb, int ya) Creates a pair profile for the given sequences with a local alignment.
SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given sequences with a global alignment.
SimpleSequencePair(S query, S target, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Creates a pair profile for the given sequences with a global alignment.

Uses of AlignedSequence.Step in org.biojava.nbio.core.alignment.template

Methods in org.biojava.nbio.core.alignment.template that return AlignedSequence.Step

Modifier and Type	Method and Description
static AlignedSequence.Step	AlignedSequence.Step.valueOf(String name) Returns the enum constant of this type with the specified name.
static AlignedSequence.Step[]	AlignedSequence.Step.values() Returns an array containing the constants of this enum type, in the order they are declared.